Dataset Information

Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C.

ABSTRACT: The PI3K/Akt pathway promotes skeletal muscle growth and myogenic differentiation. Although its importance in skeletal muscle biology is well documented, many of its substrates remain to be identified. We here studied PI3K/Akt signaling in contracting skeletal muscle cells by quantitative phosphoproteomics. We identified the extended basophilic phosphosite motif RxRxxp[S/T]xxp[S/T] in various proteins including filamin-C (FLNc). Importantly, this extended motif, located in a unique insert in Ig-like domain 20 of FLNc, is doubly phosphorylated. The protein kinases responsible for this dual-site phosphorylation are Akt and PKC?. Proximity proteomics and interaction analysis identified filamin A-interacting protein 1 (FILIP1) as direct FLNc binding partner. FILIP1 binding induces filamin degradation, thereby negatively regulating its function. Here, dual-site phosphorylation of FLNc not only reduces FILIP1 binding, providing a mechanism to shield FLNc from FILIP1-mediated degradation, but also enables fast dynamics of FLNc necessary for its function as signaling adaptor in cross-striated muscle cells.

SUBMITTER: Reimann L

PROVIDER: S-EPMC7244511 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C.

Reimann Lena L Schwäble Anja N AN Fricke Anna L AL Mühlhäuser Wignand W D WWD Leber Yvonne Y Lohanadan Keerthika K Puchinger Martin G MG Schäuble Sascha S Faessler Erik E Wiese Heike H Reichenbach Christa C Knapp Bettina B Peikert Christian D CD Drepper Friedel F Hahn Udo U Kreutz Clemens C van der Ven Peter F M PFM Radziwill Gerald G Djinović-Carugo Kristina K Fürst Dieter O DO Warscheid Bettina B

Communications biology 20200522 1

The PI3K/Akt pathway promotes skeletal muscle growth and myogenic differentiation. Although its importance in skeletal muscle biology is well documented, many of its substrates remain to be identified. We here studied PI3K/Akt signaling in contracting skeletal muscle cells by quantitative phosphoproteomics. We identified the extended basophilic phosphosite motif RxRxxp[S/T]xxp[S/T] in various proteins including filamin-C (FLNc). Importantly, this extended motif, located in a unique insert in Ig- ...[more]

PMID: 32444788

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Project description:Protein phosphorylation, driven by specific recognition of substrates by kinases and phosphatases, plays central roles in a variety of important cellular processes such as signaling and enzyme activation. Mass spectrometry enables the determination of phosphorylated peptides (and thereby proteins) in scenarios ranging from targeted in vitro studies to in vivo cell lysates under particular conditions. The characterization of commonalities among identified phosphopeptides provides insights into the specificities of the kinases involved in a study. Several algorithms have been developed to uncover linear motifs representing position-specific amino acid patterns in sets of phosphopeptides. To more fully capture the available information, reduce sensitivity to both parameter choices and natural experimental variation, and develop more precise characterizations of kinase specificities, it is necessary to determine all statistically significant motifs represented in a dataset.We have developed MMFPh (Maximal Motif Finder for Phosphoproteomics datasets), which extends the approach of the popular phosphorylation motif software Motif-X (Schwartz and Gygi, 2005) to identify all statistically significant motifs and return the maximal ones (those not subsumed by motifs with more fixed amino acids). In tests with both synthetic and experimental data, we show that MMFPh finds important motifs missed by the greedy approach of Motif-X, while also finding more motifs that are more characteristic of the dataset relative to the background proteome. Thus MMFPh is in some sense both more sensitive and more specific in characterizing the involved kinases. We also show that MMFPh compares favorably to other recent methods for finding phosphorylation motifs. Furthermore, MMFPh is less dependent on parameter choices. We support this powerful new approach with a web interface so that it may become a useful tool for studies of kinase specificity and phosphorylation site prediction.A web server is at www.cs.dartmouth.edu/~cbk/.

Dataset Information

Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C.

Publications

Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C.

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